Enabling International Collaboration using the
Eureka Research Workbench
Stuart J. Chalk1, Robert Belford2, Phuc Tran2, and Thanit Pewnim3
(1) Department of Chemistry, University of North Florida, USA(2) Department of Chemistry, UALR, Little Rock, AR 72204, USA
(3) Department of Chemistry, Silpakorn University, [email protected]
2014 Fall ACS Meeting
Lessons LearnedEnabling InternationalCollaboration using the
Eureka Research WorkbenchStuart J. Chalk1, Robert Belford2, Phuc Tran2, and Thanit
Pewnim3
(1) Department of Chemistry, University of North Florida, USA(2) Department of Chemistry, UALR, Little Rock, AR 72204, USA
(3) Department of Chemistry, Silpakorn University, [email protected]
2014 Fall ACS Meeting
Motivation What is Eureka? ExptML Web Interface Collaboration Requirements Progress Feedback Lessons Learned Future Plans Conclusion
Outline
Downloaded from glasbergen.com
Motivation
Science needs to be brought into the 21st century…at least as far as laboratory notebooks are concerned
Academics need a cheap (free) equivalent to ELN’s that are available in industry
Leverage current web technologies
Enable global collaboration
Students need a ‘social media’ app for science
Here is some research about urine
Scientists need to move todigital notebooks…
...and record not just the databut the flow and context
How science is doneis important for searching,aggregation, meta-analysis
We need more than an electronic version of a notebook
We need a science version of “Second Life” (SciLife?)
Electronic Notebooks
Started in 2006 after getting involved in the Analytical Information Markup Language (AnIML) project
Store all research notes/data in a digital format Capture the workflow of scientists Writing in a lab notebook is equivalent to
“multi-type” blogging in the digital world How to capture information? Many data types!
(ExptML) How to store files “online”? (Fedora-Commons) How to access files in the browser? (CakePHP) How to represent laboratory resources? (ExptML) How to link data together? RDF (in Fedora-Commons)
Eureka Research Workbench (ERW)
A specification (written in XML) that describes different types of information recorded during the scientific process (http://exptml.sourceforge.net)
Experiment Markup Language (ExptML)
Sample Solution Space Specimen Substance Task Template Timeline User Vendor
Annotation Api Calculation Chemical Citation Customer Data Dataset Definition Element
Equipment Event Experiment Group Message Project Protocol Quote Report Result
Collaboration
Nonylphenol ethoxylates (NPEs) or octylphenol ethoxylates (OPEs) in detergents mimic estrogens. These endocrine disrupting chemicals (EDCs) are problematic to the environment. Interested in finding out if a microalga, Chlorella vulgaris is able to biotransform NPEs.*
Sample collection in Thailand (extracts shipped to UALR)
Chemical analysis (GC-MS) at UALR
Research entered in ERW hosted at UNF
Unique identifiers for samples and extracts Record
Sample and extract information Procedures for sample collection, extraction,
sample prep, analysis Chemicals used Analysis data
All research groups can see all data
Requirements
Progress Registration of users Project, experiment, task creation Addition of substances, chemicals, solutions,
equipment Upload of
Data (different formats) Citations (research papers, procedures)
Real time testing demonstrated technical difficulties
We are still working on resolving these…
Feedback In Laboratory view, why is ‘vendors’ shown? In Notebook view, add ‘Initial procedure’
-> scratchpad (place to doodle, not add to notebook)
Ability to delete data that is ‘not needed’-> identify data as ‘junk’
Difficult to understand the difference between ‘substance’ and ‘chemical’
View data by research group (not just user) View data by project (across multiple research
groups)
Lessons Learned Speak the same language Challenge is to capture the many ways
scientists think about science Users expect to view data in any file format Users just want it to work (‘Apple-like’)
Develop introductory material for users to evaluate how they do science – from an informatics perspective
Provide video (screencast) tutorials Provide in-built help Design the system to be more flexible to fit users Develop a ‘discussion forum’ for users
Future Plans
All of the above
Add viewers for all common instrument data types
Use CakePHP’s Internationalization functions to change the language of the website interface elements
Integrate Google translate to automatically convert text when viewed by a user of another language
Conclusion International collaboration is hard
We need to speak the same language in science get the informatics perspective out of design of
interface provide functional to translate language
Provide tools that foster collaboration… … that respect issues of privacy and
provenance
[email protected] Phone: 904-620-5311 Skype: stuartchalk LinkedIn/Slidehare: https://www.linkedin.com/in/
stuchalk ORCID: http://orcid.org/0000-0002-0703-7776 ResearcherID:
http://www.researcherid.com/rid/D-8577-2013
Questions?